- I don't know if the term "emulated" is correct, but anyway let's assume it is.
- The Playstation version of (NES) Mega Man has no sprite flickering or even game slowdowns. Some screen transitions are perfect, meaning no "garbaged" things during that time. Yes, it's a matter of turning off then on the screen while doing a CHR bankswitching... and so on.
- Any thoughts about eliminating such annoyances while emulating a game?
Make a modified emulator that gives lots of extra vblank time, and has a clean scanline interrupt system, then modify the game code to take advantage of this. Of course you'll have the original source code to the game, and you'll be using games that presumably don't do lots of tricky hardware stuff.
Who told you that Capcom wrote an emulator ? Maybe (probably) they just ported the game engine on Playstation proprely (without dealing with assembly any more), and make it so that it looks like the NES, minus the bugs.
I've never played them on the Playstation (release in Japan only) so I don't know, but I remember trying them on Game Cube (aniversary collection) once, and Mega Man had a rapid fire function. Also the sound was kind of filtered as opposed to its NES counterpart if I remember correctly. But the GC has a terrible controller.
It's been a while since I've played/read about it, but it's my understanding that the Anniversary Collection NES games are not emulated, but rather rewritten for the target platform. At the very least, the sound isn't emulated, due to the fact that you can rapid-fire an enemy and hear lots of overlapping sound effects (not possible on the NES due to the limited number of channels). Even more telling is the fact that the music eventually fades out and restarts.
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Make a modified emulator that gives lots of extra vblank time
Nesticle, the emulator we all love to bash for inaccuracy, already supports this. Just adjust the values in the "timing" menu and you should be able to eliminate slowdowns in Megaman and other poorly optimized games.